Contacts of the strand formed by residues 186 - 192 (chain D) in PDB entry 1R4N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 186 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C ASP* 2.9 39.1 + - - +
178C ASN* 5.9 1.8 - - - +
182D THR* 3.7 1.2 - - - -
183D GLU 3.0 35.1 + - - +
185D PHE* 1.3 82.5 - - + +
187D GLY* 1.3 58.6 + - - +
295D THR* 3.8 5.7 - - - +
323D VAL* 6.0 1.3 - - + -
324D PHE 3.2 7.6 - - - +
325D ASN* 3.6 22.2 - - - +
327D VAL* 5.2 1.3 - - - -
108J LEU* 4.7 12.0 - - + +
140J GLN* 6.1 0.8 - - - +
171J LEU* 4.7 20.8 - - + +
173J LEU* 3.4 15.9 - - + -
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Residues in contact with GLY 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D GLY 3.2 11.2 - - - -
182D THR* 4.2 0.4 - - - -
186D LYS* 1.3 74.8 - - - +
188D ASN* 1.3 57.7 + - - +
295D THR* 4.6 1.6 - - - -
299D ILE* 3.5 17.7 - - - -
323D VAL* 3.5 2.8 - - - +
324D PHE* 2.7 34.8 + - - +
173J LEU* 3.0 16.3 - - - +
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Residues in contact with ASN 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D ASP* 4.1 8.1 + - - +
180D GLY* 3.5 1.4 - - - -
181D GLY* 2.7 40.8 + - - +
187D GLY* 1.3 73.0 - - - +
189D ALA* 1.3 60.3 + - - +
190D ARG* 4.3 16.2 - - - +
207D TYR* 4.8 0.4 + - - -
299D ILE* 3.3 7.2 - - - +
321D TYR* 3.5 22.8 + - + +
322D LEU 3.0 14.1 - - - +
323D VAL* 4.4 0.7 - - - -
171J LEU 4.0 13.2 - - - +
172J ALA* 4.0 1.5 - - - +
173J LEU* 2.9 45.7 + - + +
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ILE* 5.8 0.2 - - + -
179D ASP 3.4 5.2 - - - -
188D ASN* 1.3 75.6 - - - +
190D ARG* 1.3 62.7 + - - +
299D ILE* 4.1 8.5 - - + +
302D VAL* 3.9 25.4 - - + -
303D CYS* 3.9 24.5 - - - -
318D LEU* 4.5 2.5 - - + +
321D TYR* 3.4 3.7 - - - -
322D LEU* 2.9 37.4 + - + +
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Residues in contact with ARG 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ILE* 3.4 9.4 - - - +
179D ASP* 3.0 60.0 + - + +
188D ASN* 4.3 11.5 - - - +
189D ALA* 1.3 74.2 - - - +
191D VAL* 1.3 64.9 + - - +
192D ILE* 4.7 11.5 - - + +
199D CYS 4.0 1.6 + - - -
200D ILE* 3.6 31.5 + - - +
203D THR* 2.5 39.4 + - - -
206D LEU* 5.5 0.4 - - - +
207D TYR* 3.1 31.9 + - - -
318D LEU* 4.3 1.8 - - - -
320D ASN 3.5 20.6 + - - +
321D TYR* 3.9 22.1 + - + +
172J ALA* 4.9 0.6 - - - +
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Residues in contact with VAL 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D LEU 4.2 2.0 - - - -
178D ILE* 4.1 8.5 - - + -
190D ARG* 1.3 77.1 - - - +
192D ILE* 1.3 76.0 + - - +
193D LEU* 4.6 11.4 - - + -
197D THR* 3.4 4.9 - - - +
306D GLU* 3.2 37.9 - - + -
310D ILE* 4.3 19.7 - - + -
317D PRO* 4.8 6.1 - - + -
318D LEU* 3.8 29.4 - - + +
320D ASN* 3.2 29.5 - - - +
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Residues in contact with ILE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D ASN* 4.6 2.0 - - - +
176D PRO* 3.4 0.9 - - - +
177D LEU* 3.1 53.1 + - + +
179D ASP* 5.4 0.2 - - + -
190D ARG* 4.7 13.0 - - + +
191D VAL* 1.3 82.1 - - - +
193D LEU* 1.3 77.7 - - - +
194D PRO* 3.4 24.5 - - + -
197D THR* 4.2 2.9 - - - -
198D ALA 3.6 16.8 - - - +
199D CYS* 4.0 9.0 - - + +
200D ILE* 3.6 47.3 - - + +
320D ASN* 5.8 0.2 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il